Tag: Annotate

RNA-eXpress 1.4.3 – Extract & Annotate Transcripts from Next Generation RNA sequencing data

RNA-eXpress 1.4.3

:: DESCRIPTION

RNA-eXpress was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis.

::DEVELOPER

Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University

:: SCREENSHOTS

RNA-eXpress

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 RNA-eXpress

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.
RNA-eXpress annotates novel transcript features in RNA-seq data.
Forster SC, Finkel AM, Gould JA, Hertzog PJ.

Annotare 1.3 – Tool for Annotating High-throughput Biomedical Investigations and Resulting data

Annotare 1.3

:: DESCRIPTION

Annotare is a tool for annotating biomedical investigations and resulting data. It is a stand-alone desktop application that features 1) a set of intuitive editor forms to create and modify annotations, 2) support for easy incorporation of terms from biomedical ontologies, 3) standard templates for common experiment types, 4) a design wizard to help create a new document, and 5) a validator that checks for syntactic and semantic violation

::DEVELOPER

Annotare Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /Mac OsX
  •  Java
  • Adobe AIR

:: DOWNLOAD

  Annotare

:: MORE INFORMATION

Citation:

Ravi Shankar et al.
Annotare – a tool for annotating high-throughput biomedical investigations and resulting data,
Bioinformatics (2010) doi: 10.1093/bioinformatics/btq462

Curator tool 3.1 – Annotate Biological Pathways based on the Reactome Schema

Curator tool 3.1

:: DESCRIPTION

Curator tool is meant for use by curators to annotate biological pathways based on the Reactome schema.

::DEVELOPER

Reactome Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Curator tool

:: MORE INFORMATION

Citation

Repbase Submitter 1.1.115 – Format & Annotate Repbase Entries

Repbase Submitter 1.1.115

:: DESCRIPTION

RepbaseSubmitteris a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  Repbase Submitter

:: MORE INFORMATION

Citation:

Kohany O, Gentles AJ, Hankus L, Jurka J
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474

Graphlet kernel 1.01 – Annotate Functional Residues in Protein Structures

Graphlet kernel 1.01

:: DESCRIPTION

Graphlet kernelis a supervised learning framework for annotating functional residues in protein structures. Each residue is represented as a vector of counts of labeled non‐isomorphic subgraphs (called graphlets) in the protein contact graph, and a similarity measure between two vertices is expressed as the inner product of their respective count vectors

::DEVELOPER

the Algorithms and Computational Biology Lab

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   Graphlet kernel

:: MORE INFORMATION

Citation:

Vladimir Vacic, Lilia Iakoucheva, Stefano Lonardi, and Predrag Radivojac
“Graphlet kernels for prediction of functional residues in protein structures”
Journal of Computational Biology. 17(1):55-72. (2010)

CHROMA 1.0 – Annotated Multiple Sequence Alignments

CHROMA 1.0

:: DESCRIPTION

CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication.CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic).

::DEVELOPER

Llew Goodstadt

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • MS Word

:: DOWNLOAD

 CHROMA for win ; for Linux

:: MORE INFORMATION

Citation

Leo Goodstadt and Chris P. Ponting
CHROMA: consensus-based colouring of multiple alignments for publication.
Bioinformatics. 2001 Sep;17(9):845-6.

PlasMapper 2.0 – Web Server for Drawing & Auto-annotating Plasmid Maps

PlasMapper 2.0

:: DESCRIPTION

PlasMapper automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format. PlasMapper supports an extensive array of display options.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PlasMapper

:: MORE INFORMATION

Citation:

Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart
“PlasMapper: a web server for drawing and auto-annotating plasmid maps”
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.

AGMIAL – Annotate Microbial Genomes

AGMIAL

:: DESCRIPTION

AGMIAL is an integrated system for bacterial genome annotation. It is currently used at INRA for the newly sequenced bacterial genomes : Lactobacillus bulgaricus, Lactobacillus sakei and Flavobacterium psychrophilum, as well as the re-annotation of Lactococcus lactis, Enterococcus faecalis and faecium.

::DEVELOPER

AGMIAL Team at Jouy-en-Josas Cedex

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

AGMIAL Source Code

:: MORE INFORMATION

Citation:

K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin JF. Gibrat.
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
Nucleic Acids Research. Jul 2006.

 

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